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United States Department of Agriculture

Agricultural Research Service

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2009 Annual Report

1a. Objectives (from AD-416)
Objective 1: Develop biological resources and computational tools to enhance characterization of the bovine genome sequence. Objective 2: Use genotypic data and resulting bovine haplotype map to enhance genetic improvement in dairy cattle through development and implementation of whole genome selection and enhanced parentage verification approaches. Objective 3: Characterize conserved genome elements and identify functional genetic variation.

1b. Approach (from AD-416)
Completion of our objectives is expected, in the short term, to result in development and implementation of genome-wide selection. Ultimately the longer term objective of QTN discovery to better understand livestock biology will require a combination of quantitative genetics, LD-MAS, genome annotation, and gene expression analyses, all of which are components of this proposal and areas of expertise in our group. Efforts to characterize genome activity and structure conservation and variation are an extension of our current research program in QTL mapping and bioinformatics. This proposal completely leverages the resources derived from the Bovine Genome and HapMap projects, for which the authors of this proposal have played prominent roles. As more of the genetic variation for a specific trait is explained, a better understanding of pleiotropic and epistatic gene action will be needed. This knowledge will be developed through characterizing changes at a very fine level combined with studies of animals with known genotype associated with phenotypes resulting from selection programs. Tools used in this characterization are likely to include, but not be limited to, gene expression patterns, protein expression or structural changes, or regulatory changes.

3. Progress Report
Formed a consortium to develop a low-density single nucleotide polymorphism (SNP) beadchip assay providing parentage discovery and genome-enhanced selection for Net Merit at a commercial target price of $5-10/animal. Completed marker selection and testing of the Illumina low-density assay. NAAB cooperators provided over 10,000 DNA samples for testing parentage discovery. Received funding ($2.5 million) from USDA, NRI RFA for whole genome selection (WGS) to continue to develop algorithms to maximize utility of the low-density panel in all cattle breeds. Genotyped 5,000 dairy cattle on the BovineSNP50 chip to further refine genome enhanced predictions of genetic merit across dairy breeds and identify signatures of selection in Holsteins. Another 1,000 genomic DNA samples were extracted from semen and blood. Completed commercial implementation of genotyping by guiding AIPL, service providers, NAAB members, and 3 breed associations in standardization of commercially-produced genotypes. Continued development of alternative methods for estimating genome-enhanced genetic predictions. Completed identification of genomic signatures of selection, and results show that selection for milk yield has led to an increase in alleles negatively affecting fertility. Mapped the osteopetrosis disease locus to a 7-Mbp region of Chr 4 using the SNP50 genotypes from ~60 Angus DNA samples. Developed a commercial diagnostic test for a genetic variant of the SLC4A2 gene that is the probable disease causing mutation in collaboration with USMARC, Univ. of Illinois, Univ. of Nebraska, and the Red Angus Association of America. A systematic study of the cattle copy number variation (CNV) was completed using two oligonucleotide CGH arrays designed and fabricated from the bovine genome assemblies. Over 110 hybridizations identified approximately 229 CNV regions under stringent criteria. Selected CNV were confirmed by realtime qPCR and FISH. With the bovine genome consortium, completed the first genome-wide analyses of segmental duplication (SD). Selected SD events were confirmed by FISH and we determined ~3.1% (92 Mbp) of the cattle genome consists of SD. Developed a method based on previous work in primates to further classify and refine common repeat phylogeny in livestock. Initial testing in chicken identified 57 CR1 subfamilies and one novel turkey-specific CR1 subfamily. Results expand understanding of repeat evolution and potential function to the genome architecture. Led to development of an established software framework to further analyze the repeats in cattle. Done in collaboration with University of Maryland. Completed mapping and expression analysis of >300 million digital gene expression (DGE) sequence tags representing a quantitative gene expression from 100 different tissues of the genome sequencing cow and her relatives. A Gbrowse database was created and made publicly available through AgBase under a specific cooperative agreement with Mississippi State University. Developed additional data visualization tools based on Shannon entropy plots and Mondrian. Done in collaboration with USMARC and LARRL.

4. Accomplishments
1. The results of our development of the commercial genotyping tool (BovineSNP50, Illumina) continue to have a major impact on livestock research and the dairy AI industry. Awareness of the success in the development and application of beadchips to genomic research in cattle fueled development of commercial SNP beadchips (Illumina) in swine and sheep. We consulted in the development of these products based on the tools and research expertise obtained by our efforts in cattle. Furthermore, these commercialization efforts led Illumina to expand its business to include an agricultural science division to meet the demands from the research community and commercial entities in these products. The BovineSNP50 assay still is the de facto standard for cattle genomics research and genetic prediction use around the globe. Five service providers are offering commercial genotyping of the BovineSNP50 (GIVF in Fairfax, VA, GeneSeek in Lincoln, NE, Expression Analysis in RTP, NC, Genetic Visions in Madison, WI, and DNA landmarks in Canada). Since its inception in Aug. 2007, sales have surpassed 200,000 samples as this product continues to be used to evaluate genetic merit and investigate QTL positions in the genome in both dairy and beef cattle.

2. Predictions of genetic merit enhanced by genome-wide SNP genotypic data from the BovineSNP50 are official and actively used to make selection decisions on bulls by Holstein, Jersey and Brown Swiss breeders. The future benefits to industry continue to mature, but the industry has already capitalized on substantial gains in accuracies of predicted genetic value early in an animal’s life. As a result, increased genetic gain will be an almost immediate impact of this technology as superior animals are more readily identified and more intense selection pressure applied.

3. Co-developed two assemblies and a HapMap of the bovine genome. These resources are critical for future work on the bovine genome relative to WGS and mapping of causative genetic variation. The assembly co-developed with the University of Maryland contains a more precise marker order and complete coverage of the genome, which is critical for cattle genome research to move from marker to haplotype-based analyses of the bovine genome; a step critical to improve further improve accuracies of genome enhanced predictions of genetic merit and identification of causal genetic variation underlying phenotypic differences in traits of economic importance.

4. Developed the first genome-wide analysis of cattle CNV and SD. More than 70% CNV regions overlap with at least one gene and many of these genes are for immunity, defense and metabolism. Also, CNV regions show significant co-localization with SD. SD regions are particularly interesting because they have gone through ruminant lineage-specific gene amplification. Their copy number polymorphisms reveal that these cattle CNV may contribute to ruminant speciation and adaptation, suggesting selective pressures of ruminant diet and larger exposure to pathogen may drive acquisition or retention of specific gene dosage alterations.

5. Supported genomics research at Beltsville in a multitude of species and applications. Our unit provides scientific, computing, labor, and bioinformatic support for projects at Beltsville that want to incorporate next-generation sequencing applications into their investigations. Over the past year, our efforts have been highlighted by other researchers through the discovery of more than 200,000 SNP in soybeans, the first metagenomic studies of the bovine rumen, and production of a de novo genome sequence assembly for Turkey.

Review Publications
Zhang, W., Ding, J., Qu, Y., Hu, H., Lin, M., Datta, A., Larson, A., Liu, G., Li, B. 2008. Genomic expression analysis by single-cell mRNA differential display of quiescent CD8 T cells from tumor-infiltrating lymphocytes obtained from in vivo liver tumours. Immunology. 127(1):83-90.

Liu, G., Weirauch, M., Van Tassell, C.P., Li, R.W., Sonstegard, T.S., Matukumalli, L.K., Connor, E.E., Hanson, R.W., Yang, J. 2008. Identification of conserved regulatory elements in mammalian promoter regions: a case study using the PCK1 promoter. Genomics, Proteomics and Bioinformatics. 6(3-4):129-143.

Yu, Y., Zhang, H.M., Byerly, M.S., Bacon, L.D., Porter, T.E., Liu, G.E., Song, J. 2009. Alternative Splicing Variants and DNA Methylation Status of BDNF in Inbred Chicken Lines. Brain Research. 1269(7):1-10.

Liu, G., Alkan, C., Zhao, S., Eichler, E.E. 2009. Comparative Analysis of Alu Repeats in Primate Genomes. Genome Research. 19(5):876-885.

Van Raden, P.M., Van Tassell, C.P., Wiggans, G.R., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., Schenkel, F.S. 2009. Invited Review: Reliability of Genomic Predictions for North American Holstein Bulls. Journal of Dairy Science. 92(1):16-24.

Wiggans, G.R., Sonstegard, T.S., Van Raden, P.M., Matukumalli, L.K., Schnabel, R.D., Taylor, J.F., Schenkel, F.S., Van Tassell, C.P. 2009. Selection of single-nucleotide polymorphisms and quality of genotypes used in genomic evaluation of dairy cattle in the United States and Canada. Journal of Dairy Science. 92(7):3431-3436.

Liu, G., Li, R.W., Sonstegard, T.S., Matukumalli, L.K., Silva, M.V., Van Tassell, C.P. 2008. Characterization of a novel microdeletion polymorphism on BTA5 in cattle. Animal Genetics. 39(6):655-658.

Cole, J.B., Van Raden, P.M., O'Connell, J.R., Van Tassell, C.P., Sonstegard, T.S., Schnabel, R.D., Taylor, J.F., Wiggans, G.R. 2009. Distribution and Location of Genetic Effects for Dairy Traits. Journal of Dairy Science. 92(6):2931-2946.

McDaneld, T.G., Smith, T.P., Doumit, M.E., Miles, J.R., Coutinho, L.L., Sonstegard, T.S., Matukumalli, L.K., Nonneman, D.J., Wiedmann, R.T. 2009. MicroRNA Transcriptome Profiles During Swine Skeletal Muscle Development. Biomed Central (BMC) Genomics. 10:77.

Liu, G., Jiang, L., Tian, F., Zhu, B., Song, J. 2009. Calibration of mutation rates reveals diverse subfamily structure of galliform CR1 repeats. Genome Biology and Evolution. 2009:119-130.

Wang, S., Sha, Z., Sonstegard, T.S., Liu, H., Xu, P., Somridhavej, B., Peatmen, E., Kucuktas, H., Liu, Z. 2008. Quality assessment parameters for EST-derived SNPs from catfish. Biomed Central (BMC) Genomics. 30(9):450.

Liu, G. 2009. Applications and Case Studies of the Next-Generation Sequencing Technologies in Food, Mutrition and Agriculture. Recent Patents on Food, Nutrition & Agriculture. 1(1):75-79.

Matukumalli, L.K., Lawley, C.T., Schnabel, R.D., Taylor, J.F., Allan, M.F., Heaton, M.P., O'Connell, J., Moore, S.S., Smith, T.P., Sonstegard, T.S., Van Tassell, C.P. 2009. Development and Characterization of a High Density SNP Genotyping Assay for Cattle. PLoS One. 4(4):e5350. Available:

Elsik, C.G., Gibbs, R., Skow, L., Tellam, R., Weinstock, G., Worley, K., Kappes, S.M., Green, R.D., Alexander, L.J., Bennett, G.L., Carroll, J.A., Chitko Mckown, C.G., Hamernik, D.L., Harhay, G.P., Keele, J.W., Liu, G., Macneil, M.D., Matukumalli, L.K., Rijnkels, M., Roberts, A.J., Smith, T.P., Snelling, W.M., Stone, R.T., Waterman, R.C., White, S.N. 2009. The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution. Science. 324:522-528.

Gibbs, R., Van Tassell, C.P., Weinstock, G.M., Green, R.D., Hamernik, D.L., Kappes, S.M., Liu, G., Matukumalli, L.K., Matukumalli, A., Sonstegard, T.S., Silva, M.V. 2009. Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds. Science. 24:528-532.

Regitano, L.C., Ibelli, A.M., Gasparin, G., Miyata, M., Azevedo, A.L., Coutinho, L.L., Teodoro, R.L., Machado, M.A., Silva, M.V., Nakata, L.C., Zaros, L.G., Sonstegard, T.S., Silva, A.M., Alencar, M.M., Oliveira, M.C. 2008. On the search for markers of tick resistance in bovines. Developments in Biologicals. 132:225-230.

Mckay, S.D., Schnabel, R.D., Murdoch, B.M., Matukumalli, L.K., Aerts, J., Coppieters, W., Crews, D., Neto, E.D., Gill, C.A., Gao, C., Mannen, H., Stothard, P., Wang, Z., Van Tassell, C.P., Williams, J.L., Taylor, J.F., Moore, S.S. 2007. Whole genome linkage disequilibrium maps in cattle. Journal of Animal Breeding and Genetics. 25(8):74.

Villa-Angulo, R., Matukumalli, L.K., Gill, C.A., Choi, J., Van Tassell, C.P., Grefenstette, J.J. 2009. High-resolution haplotype block structure in the cattle genome. Journal of Animal Breeding and Genetics. 24(10):19.

Mckay, S.E., Schnabel, R.D., Murdoch, B.M., Matukumalli, L.K., Aerts, J., Coppieters, W., Crews, D., Neto, E.D., Gill, C.A., Gao, C., Mannen, H., Wang, Z., Van Tassell, C.P., Williams, J.L., Taylor, J.F., Moore, S.S. 2008. An assessment of population structure in eight breeds of cattle using a whole genome SNP panel. Journal of Animal Breeding and Genetics. 20(9):37.

Tellam, R.L., Lemay, D.G., Van Tassell, C.P., Lewin, H.A., Worley, K.C., Elsik, C.G. 2009. Unlocking the bovine genome. BioMed Central (BMC) Genetics. 24(10):193.

Zimin, A.V., Delcher, A.L., Florea, L., Kelley, D.R., Schatz, M.C., Puiu, D., Hanrahan, F., Pertea, G., Van Tassell, C.P., Sonstegard, T.S., Marcais, G., Roberts, M., Subramanian, P., Yorke, J.A., Salzberg, S.L. 2009. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biology. 10(4):R42.

Last Modified: 2/23/2016
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